Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationColourGradientTest	38	96	27	1.0100%	Show methods

Class AnnotationColourGradientTest

Class AnnotationColourGradientTest	Line # 38	Total Statements 96	Complexity 27	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	5858	10.010	2.02	1.0 1.0100%
testShadeCalculation_noThreshold() : void   testShadeCalculation_noThreshold() : void	8383	5.05	2.02	1.0 1.0100%
testShadeCalculation_aboveThreshold() : void   testShadeCalculation_aboveThreshold() : void	103103	23.023	4.04	1.0 1.0100%
testShadeCalculation_belowThreshold() : void   testShadeCalculation_belowThreshold() : void	164164	22.022	4.04	1.0 1.0100%
testFindColour_aboveThreshold() : void   testFindColour_aboveThreshold() : void	226226	12.012	5.05	1.0 1.0100%
testFindColour_belowThreshold() : void   testFindColour_belowThreshold() : void	267267	11.011	5.05	1.0 1.0100%
testFindColour_noThreshold() : void   testFindColour_noThreshold() : void	300300	6.06	2.02	1.0 1.0100%
testFindColour_originalColours() : void   testFindColour_originalColours() : void	319319	7.07	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2112676	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_aboveThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_aboveThreshold	1PASS
	0.20422535	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_belowThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_belowThreshold	1PASS
	0.14788732	jalview.schemes.AnnotationColourGradientTest.testFindColour_aboveThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_aboveThreshold	1PASS
	0.14084508	jalview.schemes.AnnotationColourGradientTest.testFindColour_belowThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_belowThreshold	1PASS
	0.08450704	jalview.schemes.AnnotationColourGradientTest.testFindColour_originalColoursjalview.schemes.AnnotationColourGradientTest.testFindColour_originalColours	1PASS
	0.06338028	jalview.schemes.AnnotationColourGradientTest.testFindColour_noThresholdjalview.schemes.AnnotationColourGradientTest.testFindColour_noThreshold	1PASS
	0.056338027	jalview.schemes.AnnotationColourGradientTest.testShadeCalculation_noThresholdjalview.schemes.AnnotationColourGradientTest.testShadeCalculation_noThreshold	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.schemes;
22
23		import static org.testng.Assert.assertEquals;
24
25		import jalview.datamodel.Alignment;
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.Annotation;
29		import jalview.datamodel.GraphLine;
30		import jalview.datamodel.Sequence;
31		import jalview.datamodel.SequenceI;
32
33		import java.awt.Color;
34
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (142) Complexity: 27 Complexity Density: 0.28
38		public class AnnotationColourGradientTest
39		{
40		final static int WIDTH = 11;
41
42		final static int THRESHOLD_FIVE = 5;
43
44		private AlignmentAnnotation ann;
45
46		private SequenceI seq;
47
48		private AlignmentI al;
49
50		Color minColour = new Color(50, 200, 150);
51
52		Color maxColour = new Color(150, 100, 250);
53
54		/**
55		* Setup creates an annotation over 11 columns with values 0-10 and threshold
56		* 5
57		*/
		100% Uncovered Elements: 0 (12) Complexity: 2 Complexity Density: 0.2
58	1	@BeforeClass(alwaysRun = true)...
59		public void setUp()
60		{
61	1	Annotation[] anns = new Annotation[WIDTH];
62		/*
63		* set annotations with values 0-10, graded colours
64		*/
65	12	for (int col = 0; col < WIDTH; col++)
66		{
67	11	int hue = col * 20;
68	11	Color colour = new Color(hue, hue, hue);
69	11	anns[col] = new Annotation("a", "a", 'a', col, colour);
70		}
71
72	1	seq = new Sequence("Seq", "");
73	1	al = new Alignment(new SequenceI[] { seq });
74
75		/*
76		* AlignmentAnnotation constructor works out min-max range
77		*/
78	1	ann = new AlignmentAnnotation("", "", anns);
79	1	ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
80	1	seq.addAlignmentAnnotation(ann);
81		}
82
		100% Uncovered Elements: 0 (7) Complexity: 2 Complexity Density: 0.4 1PASS
83	1	@Test(groups = "Functional")...
84		public void testShadeCalculation_noThreshold()
85		{
86	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
87		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
88	12	for (int col = 0; col < WIDTH; col++)
89		{
90	11	Color result = testee.shadeCalculation(ann, col);
91		/*
92		* column <n> is n/10 of the way from minCol to maxCol
93		*/
94	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
95		150 + 10 * col);
96	11	assertEquals(result, expected, "for column " + col);
97		}
98		}
99
100		/**
101		* Test the 'colour above threshold' case
102		*/
		100% Uncovered Elements: 0 (29) Complexity: 4 Complexity Density: 0.17 1PASS
103	1	@Test(groups = "Functional")...
104		public void testShadeCalculation_aboveThreshold()
105		{
106	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
107		minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
108	12	for (int col = 0; col < WIDTH; col++)
109		{
110	11	Color result = testee.shadeCalculation(ann, col);
111		/*
112		* colour is derived regardless of the threshold value
113		* (the renderer will suppress colouring if above/below threshold)
114		*/
115	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
116		150 + 10 * col);
117	11	assertEquals(result, expected, "for column " + col);
118		}
119
120		/*
121		* now make 6-10 the span of the colour range
122		* (annotation value == column number in this test)
123		*/
124	1	testee.setThresholdIsMinMax(true);
125	6	for (int col = 0; col < THRESHOLD_FIVE; col++)
126		{
127		/*
128		* colours below the threshold are computed as before
129		*/
130	5	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
131		150 + 10 * col);
132	5	Color result = testee.shadeCalculation(ann, col);
133	5	assertEquals(result, expected, "for column " + col);
134		}
135	7	for (int col = THRESHOLD_FIVE; col < WIDTH; col++)
136		{
137		/*
138		* colours for values >= threshold are graduated
139		* range is 6-10 so steps of 100/5 = 20
140		*/
141	6	int factor = col - THRESHOLD_FIVE;
142	6	Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
143		150 + 20 * factor);
144	6	Color result = testee.shadeCalculation(ann, col);
145	6	assertEquals(result, expected, "for column " + col);
146		}
147
148		/*
149		* test for boundary case threshold == graphMax (JAL-3206)
150		*/
151	1	float thresh = ann.threshold.value;
152	1	ann.threshold.value = ann.graphMax;
153	1	Color result = testee.shadeCalculation(ann, WIDTH - 1);
154	1	assertEquals(result, maxColour);
155	1	testee.setThresholdIsMinMax(false);
156	1	result = testee.shadeCalculation(ann, WIDTH - 1);
157	1	assertEquals(result, maxColour);
158	1	ann.threshold.value = thresh; // reset
159		}
160
161		/**
162		* Test the 'colour below threshold' case
163		*/
		100% Uncovered Elements: 0 (28) Complexity: 4 Complexity Density: 0.18 1PASS
164	1	@Test(groups = "Functional")...
165		public void testShadeCalculation_belowThreshold()
166		{
167	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
168		minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
169
170	12	for (int col = 0; col < WIDTH; col++)
171		{
172	11	Color result = testee.shadeCalculation(ann, col);
173		/*
174		* colour is derived regardless of the threshold value
175		* (the renderer will suppress colouring if above/below threshold)
176		*/
177	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
178		150 + 10 * col);
179	11	assertEquals(result, expected, "for column " + col);
180		}
181
182		/*
183		* now make 0-5 the span of the colour range
184		* (annotation value == column number in this test)
185		*/
186	1	testee.setThresholdIsMinMax(true);
187	6	for (int col = THRESHOLD_FIVE + 1; col < WIDTH; col++)
188		{
189		/*
190		* colours above the threshold are computed as before
191		*/
192	5	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
193		150 + 10 * col);
194	5	Color result = testee.shadeCalculation(ann, col);
195	5	assertEquals(result, expected, "for column " + col);
196		}
197
198	7	for (int col = 0; col <= THRESHOLD_FIVE; col++)
199		{
200		/*
201		* colours for values <= threshold are graduated
202		* range is 0-5 so steps of 100/5 = 20
203		*/
204	6	Color expected = new Color(50 + 20 * col, 200 - 20 * col,
205		150 + 20 * col);
206	6	Color result = testee.shadeCalculation(ann, col);
207	6	assertEquals(result, expected, "for column " + col);
208		}
209
210		/*
211		* test for boundary case threshold == graphMin (JAL-3206)
212		*/
213	1	float thresh = ann.threshold.value;
214	1	ann.threshold.value = ann.graphMin;
215	1	Color result = testee.shadeCalculation(ann, 0);
216	1	assertEquals(result, minColour);
217	1	testee.setThresholdIsMinMax(false);
218	1	result = testee.shadeCalculation(ann, 0);
219	1	assertEquals(result, minColour);
220	1	ann.threshold.value = thresh; // reset
221		}
222
223		/**
224		* Test the 'colour above threshold' case
225		*/
		100% Uncovered Elements: 0 (20) Complexity: 5 Complexity Density: 0.42 1PASS
226	1	@Test(groups = "Functional")...
227		public void testFindColour_aboveThreshold()
228		{
229	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
230		minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
231	1	testee = (AnnotationColourGradient) testee.getInstance(null, al);
232
233	12	for (int col = 0; col < WIDTH; col++)
234		{
235	11	Color result = testee.findColour('a', col, seq);
236		/*
237		* expect white at or below threshold of 5
238		*/
239	11	Color expected = col <= 5 ? Color.white
240		: new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
241	11	assertEquals(result, expected, "for column " + col);
242		}
243
244		/*
245		* now make 6-10 the span of the colour range
246		* (annotation value == column number in this test)
247		*/
248	1	testee.setThresholdIsMinMax(true);
249	12	for (int col = 0; col < WIDTH; col++)
250		{
251		/*
252		* colours for values > threshold are graduated
253		* range is 6-10 so steps of 100/5 = 20
254		*/
255	11	int factor = col - THRESHOLD_FIVE;
256	11	Color expected = col <= 5 ? Color.white
257		: new Color(50 + 20 * factor, 200 - 20 * factor,
258		150 + 20 * factor);
259	11	Color result = testee.findColour('a', col, seq);
260	11	assertEquals(result, expected, "for column " + col);
261		}
262		}
263
264		/**
265		* Test the 'colour below threshold' case
266		*/
		100% Uncovered Elements: 0 (19) Complexity: 5 Complexity Density: 0.45 1PASS
267	1	@Test(groups = "Functional")...
268		public void testFindColour_belowThreshold()
269		{
270	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
271		minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
272	1	testee = (AnnotationColourGradient) testee.getInstance(null, al);
273
274	12	for (int col = 0; col < WIDTH; col++)
275		{
276	11	Color result = testee.findColour('a', col, seq);
277	11	Color expected = col >= 5 ? Color.white
278		: new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
279	11	assertEquals(result, expected, "for column " + col);
280		}
281
282		/*
283		* now make 0-5 the span of the colour range
284		* (annotation value == column number in this test)
285		*/
286	1	testee.setThresholdIsMinMax(true);
287	12	for (int col = 0; col < WIDTH; col++)
288		{
289		/*
290		* colours for values < threshold are graduated
291		* range is 0-5 so steps of 100/5 = 20
292		*/
293	11	Color expected = col >= 5 ? Color.white
294		: new Color(50 + 20 * col, 200 - 20 * col, 150 + 20 * col);
295	11	Color result = testee.findColour('a', col, seq);
296	11	assertEquals(result, expected, "for column " + col);
297		}
298		}
299
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33 1PASS
300	1	@Test(groups = "Functional")...
301		public void testFindColour_noThreshold()
302		{
303	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
304		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
305	1	testee = (AnnotationColourGradient) testee.getInstance(null, al);
306
307	12	for (int col = 0; col < WIDTH; col++)
308		{
309	11	Color result = testee.findColour('a', col, seq);
310		/*
311		* column <n> is n/10 of the way from minCol to maxCol
312		*/
313	11	Color expected = new Color(50 + 10 * col, 200 - 10 * col,
314		150 + 10 * col);
315	11	assertEquals(result, expected, "for column " + col);
316		}
317		}
318
		100% Uncovered Elements: 0 (11) Complexity: 3 Complexity Density: 0.43 1PASS
319	1	@Test(groups = "Functional")...
320		public void testFindColour_originalColours()
321		{
322	1	AnnotationColourGradient testee = new AnnotationColourGradient(ann,
323		minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
324	1	testee = (AnnotationColourGradient) testee.getInstance(null, al);
325
326		/*
327		* flag corresponding to 'use original colours' checkbox
328		* - just use the individual annotation colours
329		*/
330	1	testee.setPredefinedColours(true);
331
332		/*
333		* the annotation colour is returned, except for column 0 where it is
334		* black - in this case the colour scheme colour overrides it
335		*/
336	12	for (int col = 0; col < WIDTH; col++)
337		{
338	11	int hue = col * 20;
339	11	Color c = col == 0 ? minColour : new Color(hue, hue, hue);
340	11	assertEquals(testee.findColour('a', col, seq), c,
341		"for column " + col);
342		}
343		}
344		}